Inferring phylogeny from sequence variation

Question 1

What are the two types of tree

Answer 1

Phenograms and phylogentic trees

Question 2

What does ultrametric mean

Answer 2

A tree with equal root to tip path lengths for all lineages

Question 3

What are cladograms

Answer 3

Y axis has no meaning

Question 4

What are additive trees

Answer 4

Y axis tells us about the amount of evolutionary change

Question 5

Whats a fully bifurcated tree

Answer 5

Assumes all speciation events involve one thing splitting into two

Question 6

What are mutlifurcated trees

Answer 6

Node splits into more than two species, could be rapid speciation event

Question 7

Why do we construct phylogenies

Answer 7

To know how species are related to eachother

Question 8

How do we add a root to a tree

Answer 8

Add information for an outgroup

Question 9

Whats an outgroup

Answer 9

A taxon that we believe to be more distantly related to the focal species than they are to one another

Question 10

All trees to consider

Answer 10

Taxa, unrooted, rooted

Question 11

How do we estimate genetic distance

Answer 11

K = porportion of nucleotide sites that are different

Question 12

Whats an UPGMA

Answer 12

unweighted pair group method with arithmetic mean

Question 13

Whats the jukes cantor distance correlation

Answer 13

The more evolutionary distance there is, the more likely there’s more hits

Question 14

Whats the Jukes cantor equation

Answer 14

Kjc = -(3/4)ln[1-(4/3)k]

Question 15

Examples of when phylogenies are useful

Answer 15

Flying mammals, did they evolve once or twice

Question 16

Limitations to phylogenetic trees

Answer 16

Trees are hypotheses
Scoring characters is hard
Homoplasy
Ancient events are hard to infer
Some lineages might be adapting too rapidly
Hybridisation may be a problem